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X-ray structure of the ROQ domain from murine Roquin-1 in complex with a 23-mer Tnf-CDE RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QI0 pdb entry 4QI0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 200 mM NaCl, 100 mM Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.56 α = 105.68 b = 60.41 β = 101.36 c = 84.37 γ = 95.72
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.03321 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 50 95.7 0.07 13.9 19951 19951
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.08 96.9 0.513 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 4QI0 3 50 18931 18931 1020 95.82 0.20549 0.20316 0.2092 0.24679 0.2473 RANDOM 77.711
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 6.29 6.88 -1.27 -5.25 0.73 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.798 r_dihedral_angle_3_deg 18.243 r_dihedral_angle_4_deg 13.619 r_long_range_B_other 13.417 r_long_range_B_refined 13.416 r_scangle_other 9.992 r_mcangle_it 8.88 r_mcangle_other 8.879 r_scbond_it 6.637 r_scbond_other 6.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.798 r_dihedral_angle_3_deg 18.243 r_dihedral_angle_4_deg 13.619 r_long_range_B_other 13.417 r_long_range_B_refined 13.416 r_scangle_other 9.992 r_mcangle_it 8.88 r_mcangle_other 8.879 r_scbond_it 6.637 r_scbond_other 6.633 r_mcbond_it 5.921 r_mcbond_other 5.908 r_dihedral_angle_1_deg 5.589 r_angle_refined_deg 1.513 r_angle_other_deg 1.166 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4895 Nucleic Acid Atoms 1576 Solvent Atoms 32 Heterogen Atoms
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling